Energy Sciences

Recent improvements in large language models (LLMs) have had a dramatic effect on capabilities and productivity across many disciplines involving critical thinking and writing. The development of the model context protocol (MCP) provides a way to extend the power of LLMs to a specific set of tasks or scientific equipment with help from curated tools and resources. Here, we describe a framework called TEM Agent designed for transmission electron microscopy (TEM) that leverages the benefits of LLMs through a MCP approach. We simultaneously access and control several subsystems of the TEM, a data management platform, and high-performance computing resources through text-based instructions. We demonstrate the abilities of the TEM Agent to set up and complete intricate workflows using a simplified set of MCP tools and resources accompanying a commercial LLM without any additional training. The use of a framework such as the TEM Agent simplifies access to complex microscope ecosystems comprised of several vendor and custom systems enhancing the ability of users to accomplish microscopy experiments across a range of difficulty levels.

ABSTRACT Achieving high‐energy‐density and long‐term cycling stability in Mn‐redox‐based cathodes is a critical step toward advancing Ni‐ and Co‐free Li‐ion chemistries to diversify supply chains and lower battery costs. Here, we demonstrate an unusually high performance benchmark for Mn‐redox cathodes using near‐micron single‐crystalline δ‐phase cation‐disordered rocksalt (δ‐DRX), derived from Mn‐rich DRX, delivering ≈640 Wh kg −1 with ≈97% capacity retention over 400 cycles. The very high energy density and cycle life were achieved by using a high Mn content, to suppress oxygen redox activity, and careful control of the synthesis parameters to tune single crystal particle size. Using high‐throughput automated electron microscopy, we identify interparticle compositional heterogeneity present in the early stage of phase‐pure DRX formation as the origin of orthorhombic LiMnO 2 impurity formation during cooling, a finding that rationalizes the long high‐temperature dwell times required and the associated particle coarsening in conventional synthesis. We demonstrate that an accelerated cooling strategy kinetically suppresses localized impurity formation, reducing long high‐temperature exposure, and enables downsizing of single‐crystalline Mn‐rich DRX particles to the near‐micron regime (D50 = 1.5 µm). This work provides a mechanistic basis for particle‐size control in Mn‐rich DRX synthesis, and presents δ‐DRX as a stable, sustainable, high‐performance, Ni‐ and Co‐free cathode material.

Abstract Bacterial microcompartments (BMCs) are self-assembling organelles that colocalize enzymes and metabolites of various biochemical pathways. Their selectively permeable shell is made entirely of protein, and the inherent properties of these systems make them attractive templates for bioengineering synthetic nanoreactors. Understanding the extent of shell stability in an extended range of conditions broadens the scope of chemistries that can be confined in these nanocompartments. Here we analyze the stability of in vitro assembled BMC shells and find that they retain their structure at high concentrations of various solvents and detergents, at temperatures up to 75 °C, and across a pH range from 3.9 to 11. Shell disassembly is observed below pH 3.9, but shells can be reassembled upon increasing the pH back to 8. These results expand the range of reactions that can be performed inside protein-based nanoreactors and underscore the potential of modular BMC shell proteins as versatile biomaterials.

Autoencoder-transformer model applicable to both simulated and experimental XAS spectra is developed to predict the oxidation state of copper. X-ray absorption spectroscopy (XAS) and electron energy-loss spectroscopy (EELS) produce detailed information about oxidation state, bonding, and coordination, making them essential for quantitative studies of redox and structure in functional materials. However, high-throughput quantitative analysis of these spectra, especially for mixed valence materials, remains challenging as diverse experimental conditions introduce noise, misalignment, and broadening of the spectral features. We address this challenge by training a machine learning model consisting of an autoencoder to standardize the spectra and a transformer model to predict both Cu oxidation state and Bader charge directly from L-edge spectra. The model is trained on a large dataset of FEFF-simulated spectra, and its performance is evaluated on both simulated and experimental data. The results of the machine learning model exhibit accurate and transferable predictions across the domains of simulated and experimental spectra. These advances enable future quantitative analysis of Cu redox processes under in situ and operando conditions.

Chiroptical properties in metal halide perovskites typically arise from asymmetric crystal structures induced by chiral organic molecules during synthesis or chiral additives. However, the synthesis of two-dimensional chiral halide perovskites with sufficiently high dissymmetry factors for practical applications remains challenging. Herein, we present a two-step ionic gel-mediated nucleation and recrystallization reaction, enabling the synthesis of nanostructured chiral halide perovskite films exhibiting large intrinsic circular dichroism dissymmetry factors (gCD) up to 10−2. The ionic gel mediates the reaction between lead(II) iodide (PbI2) and R/S-methylbenzylammonium iodide (R/S-MBAI), to facilitate the formation of higher-order iodoplumbate PbI3- and oligomeric Pb-I-MBA species, which recrystallize during heat treatment as anisotropic nanostructures without preferential orientation. Ionic gel-mediated films exhibit a very pronounced peak splitting originating from a well-defined exciton fine structure and narrow photoluminescence linewidth. This is indicative of the presence of electron-hole exchange interactions and minimized structural disorder in the material leading to significantly amplified chiroptical response. This work demonstrates a synthesis route for nanostructured chiral MBA2PbI4 films, whose unique structural feature with reduced crystalline imperfection enables amplified circular dichroism and gCD response.

Effective interfacial passivation is essential for achieving high-performance perovskite photovoltaics. 2D/3D heterostructures are a widely adopted strategy for defect passivation and band alignment regulation. Despite recent progress, achieving favorable interfacial energetics and comprehensively suppressing nonradiative recombination at both surfaces and grain boundaries continues to be an active area of investigation. We introduce a coassembled 2D architecture in which long-chain ligands are complemented by a minority component of short-chain ligands to form a mixed-ligand passivation layer. Such a coassembled structure promotes preferentially phase-pure, n = 2, 2D layer formation, resulting in an energetically favorable band alignment that enhances charge extraction. In addition, this coassembly facilitates effective passivation of interfacial defects at both surfaces and grain boundaries, leading to suppressed nonradiative recombination. As a consequence, these interfacial improvements increase carrier lifetimes and enhance the fill factor and open-circuit voltage of the device, yielding a higher power-conversion efficiency.

Effective water and thermal management are crucial for maximizing the performance of proton exchange membrane fuel cells (PEMFCs). This study presents a robust non-isothermal model that integrates two-phase flow, species transport, and heat and mass transfer phenomena to investigate water generation, accumulation, and permeation mechanisms within the gas diffusion layer (GDL) of PEMFCs. Utilizing X-ray computed tomography (XCT) reconstruction, a 2D structure of the Freudenberg GDL is generated. The model incorporates anisotropic thermal conductivity, distinguishes between in-plane and through-plane K IP K TP ratios, and demonstrates its importance to temperature distribution and subsequent condensation rate within the GDL. Additionally, our parametric analysis evaluates the effects of GDL thermal conductivity, current density, operating temperature, and pressure on water condensation and transport processes in PEMFCs. Key findings include the identification of distinct phases of condensation and transport within the porous medium under varying conditions: nucleation, growth, accumulation, and mobilization. Simulation results uncovered condensation regions within the GDL, demonstrating that temperature gradients, strongly influenced by anisotropic thermal conductivity, play a critical role in water generation and transport dynamics. The study further reveals that areas beneath the land in the GDL exhibit lower temperatures, leading to elevated condensation rates and larger droplet formation within those regions. Additionally, the interconnection of condensate droplets via wetting layers emphasizes the impact of temperature distribution on water movement. This study provides deeper insight into water vapor condensation and transport mechanisms within GDLs, informing the design and optimization of GDL structures for enhanced PEMFC performance.

Macromolecular crystallography has historically inferred models of internal crystal architecture from reciprocal-space measurements of Bragg reflections. Nevertheless, direct real-space visualization of crystallographic disorder remains elusive, particularly at the nanoscale. Using a 15-nm probe, here we apply both ambient-temperature and cryogenic four-dimensional scanning transmission electron microscopy (4D-STEM) to map the topography of coherently diffracting domains (CDDs) in lysozyme and myoglobin microcrystals at length scales 100× finer than conventional X-ray and electron beams. Virtual dark-field images show that each Bragg peak arises from spatially distinct subvolumes representing smooth and continuous variations in local lattice orientation. Under sustained irradiation, protein CDDs undergo rearrangements spanning several micrometers of internal movement. Furthermore, pinpoint high-dose "impact crater" experiments reveal delocalized radiolytic damage propagating hundreds of nanometers from primary irradiation sites, behavior similar to small-molecule crystals but amplified in both rate and magnitude. Together, these results establish macromolecular microcrystals as dynamic assemblies whose internal architecture continuously reorganizes during irradiation, laying the foundation for realistic models of mosaicity directly informed by both real-space and reciprocal-space observations.

Atomic structures of nanomaterials are inherently dynamic and continuously reshaped through interactions with chemical species and external stimuli. Such dynamics are further amplified as the size and dimensionality of nanomaterials decrease. Despite advances in analytical methods, it remains challenging to capture the structural dynamics of nanomaterials in reactive environments with both atomic spatial resolution and commensurate temporal resolution. Here, we directly visualize atomic-scale dynamics of gold (Au) nanocrystals in reactive liquid environments with millisecond-speed liquid-cell electron microscopy (EM) and deep-learning denoising. We uncover reversible fluctuations in the local crystallinity of Au nanocrystals dependent on the surrounding chemical environment. These transient fluctuations, driven by interactions at nanocrystal-liquid interfaces, critically influence the dissolution kinetics and grain boundary relaxation. By overcoming the spatiotemporal limitations in conventional liquid-cell EM, our findings provide insights into how transient nanoscale structures dictate the stability and reactivity of nanomaterials.

Solute-intercalation-induced phase separation creates spatial heterogeneities in host materials, a phenomenon ubiquitous in batteries, hydrogen storage, and other energy devices. Despite many efforts, probing intercalation processes at the atomic scale has been a significant challenge. By utilizing liquid-phase transmission electron microscopy (TEM), we study hydrogen (de)intercalation in palladium nanocrystals as a model system and have achieved unprecedented atomic-resolution imaging of hydrogen intercalation wave dynamics. Our observations reveal that intercalation wave mechanisms, instead of shrinking-core mechanisms, prevail at ambient temperature for palladium nanocubes ranging from ∼60 nm down to ∼10 nm. Systematic image analysis uncovers the atomic evolution of the hydrogen intercalation wave, transitioning from nonplanar and inclined boundaries to those closely aligned with {100} planes. Our kinetic Monte Carlo simulations demonstrate that the observed intercalation wave dynamics correspond to sorption pathways minimizing the lattice mismatch strain at the phase boundary. Unveiling the atomic intercalation pathways holds profound implications for engineering intercalation-mediated devices and advancements in energy sciences.